Nomenclature Guidelines

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Gene Nomenclature Guidelines

1. Established nomenclature for gene families has precedence over other names.
   Examples: abcA1, abcA2, abcB1, atg1, atg4. This includes Dictyostelium homologs of human genes for which a nomenclature has been established by the HGNC, or for established gene names of non-mammalian homologs, usually if there are no mammalian counterparts or if the nomenclature is better established in non-mammalian organisms.
   • 1:1 human orthologs are named using the established human name, e.g. eif3f, nmd3, dgat1.
   • Many-to-one homologs: If Dictyostelium has only one gene that is similar to a group of human genes, this gene is named dropping the numbers or letters that distinguish the group members. For example, human has PCBD1 and PCBD2, and the single Dictyostelium gene is named pcbd.
   • One-to-many homologs: If Dictyostelium has and expanded group of genes compared to other organisms with established nomenclature, additional letters or numbers maybe added to distinguish the members. For example, while human has two cytochrome b5 genes and yeast has one, Dictyostelium has 3 family members, named cyb5A-C.
   • Many-to-many homologs: It is possible to mix letter and number suffixes to distinguish cases where some members of a family are orthologs and other are Dictyotelium-specific paralogs; for example, rab21, rab7A, rab7B, are orthologs of mammalian RAB21 and RAB7, respectively, while rabH does not correspond to any mammalian RAB.
   • Exceptions where human nomenclature is discouraged are when the human name makes no sense for Dictyostelium, for example OPA3 (Optic Atrophy 3), or TEX2 (Testis Expressed 2). As more functional data becomes available, HGNC as well as UniProtKB are working to improve nomenclature.
   If it is not possible to identify an appropriate name, for the time being leave the DDB_G identifier as the gene name.
   
   
2. New gene names, especially for non conserved genes, should conform to the following conventions derived from Demerec et al. (1966). A locus description consisting of three lower-case, italicized letters, followed by a capital italicized letter to distinguish genes with the same descriptor that are related in a significant way.
   Examples: rdeA, rdeB and rdeC; or tagA, tagB and tagC.
   For large gene families (> 26 members), we encourage the use of numbers rather than letters.
   
   
3. Existing gene names remain unchanged.
   Examples: act15, mhcA, and pyr5-6.
   
   
4. Original naming authors can change any gene name by describing the name change in their next publication containing the gene and informing dictyBase.
   Example: There were several publications about the spore coat protein SP70, and even after the gene has been cloned it was still referred to as SP70. However, in the early 90ies the gene name cotB was introduced by Bill Loomis.
   
   
5. All names that are found in the literature will remain in dictyBase as synonyms.
   Example: pkaC has five synonyms: PKA, pkacat, DdPK3, DdPK2, PKA-C.

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Protein Nomenclature Guidelines

1. A protein may be named after the gene encoding it by capitalizing the first letter and without the use of italics.
   Examples: RegA (encoded by regA), RegA(D212A) (encoded by regA(D212A)).
   
   
2. A protein can also be referred to by its full name or a protein synonym.
   Examples: actin, ribonucleotide reductase small subunit, RNR, protein kinase C, PKC.
   
   
3. Proteins that have been identified by physical properties are sometimes named following this property; however this practice is discouraged because many different proteins can have the same attribute.
   Examples: p34, 34kDa protein, actin-binding protein, calcium-binding protein.

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Mutant Allele Nomenclature Guidelines

1. Allele names should be italicized and placed in parentheses following the gene name without a space.
   Examples: yakA(AK235) and yakA(AK800): different insertion mutations in the yakA gene.
   
   
2. Where the nature of the mutation is not known or only a single allele is relevant, a superscript minus sign can be used for brevity.
   Example: regA^-.
   
   
3. The use of superscripts to describe the general nature of an allele can be used but should be limited to two or three letters, e.g. ts (temperature sensitive), cs (cold sensitive), hc (high copy) or dn (dominant negative).
   Examples: regA(AK202^ts), regA^ts.
   
   
4. Amino acid substitutions should be given as the old residue in single-letter code with its codon location followed by the new (mutant) amino acid. The amino acid change is an interpretation of what the gene will produce and refers to a protein so it is not put in italics.
   Example: regA(D212A) has an alanine in place of the aspartate at position 212.
   
   
NOTE: AX4 is the reference strain for the “wild-type” amino acid sequence within proteins since it is the first strain that has been sequenced.

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Strain Nomenclature Guidelines

• Systematic Strain Name

Strains must have an unambiguous name, consisting of 2 or 3 capital letters plus a unique serial number (e.g. HM1 or HTY217). Labs or workers should always use the same capital prefixes or small group of prefixes. The prefixes are assigned by a clearinghouse upon request. See Appendix 1 for a current list of assigned strain prefixes. In the past all lab designations started with either H (for haploid) or D (for diploid) and many of these strains prefixes are still in use.
In cases where no systematic name is provided, dictyBase will automatically assign a systematic strain name consisting of the letters DBS (dictyBase Strain) followed by seven digits.

• Strain Descriptor

The strain descriptor is meant to provide a quick overview of the key genetic modifications that produced the strain, including the gene name, the promoter, the mutations, and tags or reporter genes. The strain descriptor appears on the Gene Page and on the Phenotype and Strain Details page and is meant to give a more descriptive account of strains compared to systematic strain names. The format of the strain descriptor is as follows:



gene-/[promoter]:gene(substitution or truncation):marker

where

-    represents an endogenous mutant allele, typically a null or a functional null mutant
/    represents a compound mutant
[ ]  represents the promoter gene
( )  indicates a substitution and/or a truncation
:    represents a fusion between two genes


Additional annotations may appear in brackets as follows:

[unk] represents a gene fusion to an unknown promoter
[OE] designates an overexpressor under the control of an unspecified promoter
[KD] designates an knockdown strain when the method is unknown
[AS] designates an antisense strain
[RNAi] designates an interference RNA strain
[inviable] precedes strains described as inviable

• Strain ID

All strains curated by dictyBase also have a strain ID consisting of the letters DBS (dictyBase Strain) followed by seven digits. This ID is created automatically and does not change. If there is no other Systematic Strain Name, both the Strain ID and the Systematic Strain Name will be the same.

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Phenotypes

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Genotypes

Constructs carried within cells should be described in the formal genotype of that strain and placed in brackets. Thus, a cotB promoter beta-galactosidase reporter construct in a mutant strain might have a formal genotype of “regA(AK202), [cotB/lacZ], neoR”, but could be shortened to “regA-[cotB/lacZ]” in the context of a sentence describing the strain's properties in the results section of a paper.

The following names should be used to indicate common drug resistance/sensitivity and nutrient auxotrophy/prototrophy. For clarity, relevant phenotypic markers should be included at the end of formal genotypes (no italics):

Drug resistance:

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Plasmids

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Molecular Genetic Constructs

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Chromosomes

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Management

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References

This document is based on the Nomenclature Proposal written in November 2000 by the Dictyostelium Community Organizing Committee: Adam Kuspa (Chairman), Robert R. Kay, Alan R. Kimmel, Hideko Urushihara, Richard Kessin (ex officio) Chairman.

General:

Demerec, M. et al., (1966). A proposal for a uniform nomenclature in bacterial genetics. Genetics 54:61-76.

Gene Lists:

Kuspa, A., D. Maghakian, P. Bergesch, and W.F. Loomis. 1992. Physical mapping of genes to specific chromosomes in Dictyostelium discoideum. Genomics 13:49-61.

Loomis, W.F., D. Welker, J. Hughes, D. Maghakian, and A. Kuspa. 1995. Integrated maps of the chromosomes in Dictyostelium discoideum. Genetics 141:147-157.

Kuspa, A., and W.F. Loomis. 1996. Ordered yeast artificial chromosome clones representing the Dictyostelium discoideum genome. Proc. Natl. Acad. Sci. USA 93:5562-5566.

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Appendix 1. List of Known Strain Prefixes by Laboratory

Updated March 27, 2007

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